DOCSLIB.ORG

Enterorhabdus Caecimuris Sp. Nov., a Member of the Family

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Enterorhabdus Caecimuris Sp. Nov., a Member of the Family View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central International Journal of Systematic and Evolutionary Microbiology (2010), 60, 1527–1531 DOI 10.1099/ijs.0.015016-0 Enterorhabdus caecimuris sp. nov., a member of the family Coriobacteriaceae isolated from a mouse model of spontaneous colitis, and emended description of the genus Enterorhabdus Clavel et al. 2009 Thomas Clavel,1 Wayne Duck,2 Ce´dric Charrier,3 Mareike Wenning,4 Charles Elson2 and Dirk Haller1 Correspondence 1Biofunctionality, ZIEL – Research Center for Nutrition and Food Science, Technische Universita¨t Thomas Clavel Mu¨nchen (TUM), 85350 Freising Weihenstephan, Germany [email protected] 2Division of Gastroenterology and Hepatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA 3NovaBiotics Ltd, Aberdeen, AB21 9TR, UK 4Microbiology, ZIEL – Research Center for Nutrition and Food Science, TUM, 85350 Freising Weihenstephan, Germany The C3H/HeJBir mouse model of intestinal inflammation was used for isolation of a Gram- positive, rod-shaped, non-spore-forming bacterium (B7T) from caecal suspensions. On the basis of partial 16S rRNA gene sequence analysis, strain B7T was a member of the class Actinobacteria, family Coriobacteriaceae, and was related closely to Enterorhabdus mucosicola T T Mt1B8 (97.6 %). The major fatty acid of strain B7 was C16 : 0 (19.1 %) and the respiratory quinones were mono- and dimethylated. Cells were aerotolerant, but grew only under anoxic conditions. Strain B7T did not convert the isoflavone daidzein and was resistant to cefotaxime. The results of DNA–DNA hybridization experiments and additional physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain B7T from the type strain of E. mucosicola. Therefore, strain B7T represents a novel species, for which the name Enterorhabdus caecimuris sp. nov. is proposed. The type strain is B7T (5DSM 21839T 5CCUG 56815T). The family Coriobacteriaceae currently comprises 13 caecum of a C3H/HeJBir mouse, a mouse substrain prone genera, four of which have been described recently, and to spontaneous colitis (Sundberg et al., 1994), after 3 days includes Adlercreutzia equolifaciens (Maruo et al., 2008), growth at 37 uC on ATCC medium 602 E. Additional the type species of which was isolated from human faeces; information on strain isolation and 16S rRNA gene Asaccharobacter celatus (Minamida et al., 2008), isolated sequencing has been published elsewhere (Duck et al., from a rat caecum; Enterorhabdus mucosicola (Clavel et al., 2007). Unless otherwise stated, all experiments for the 2009), isolated from the inflamed ileal mucosa of a mouse; description of strain B7T were carried out as described and Gordonibacter pamelaeae (Wu¨rdemann et al., 2009), previously (Clavel et al., 2009). Bacteroides vulgatus was isolated from a patient with Crohn’s disease. used as a positive control for the determination of growth with bile salts (no. 48305; Fluka). Cellular fatty acids, During the course of experiments focused on flagellated respiratory quinones, peptidoglycan and whole-cell sugars bacteria and their implication in intestinal inflammation T were analysed by the DSMZ, Braunschweig, Germany, (Duck et al., 2007), strain B7 was isolated from the according to standard procedures (Sasser, 1990; Cashion et al., 1977; De Ley et al., 1970; Huß et al., 1983; Mesbah Abbreviation: FT-IRS, Fourier-transform infrared spectroscopy. et al., 1989; Rhuland et al., 1955; Staneck & Roberts, 1974; The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and Tamaoka & Komagata, 1984; Visuvanathan et al., 1989; T gyrase B gene sequences of strain B7 are DQ789120 and Whiton et al., 1985). GQ409830, respectively. T Supplementary figures showing the polar lipid compositions and daidzein 16S rRNA gene sequences from strain B7 (determined as conversion abilities of strain B7T and the type strain of Enterorhabdus described previously; Duck et al., 2007) and GenBank were mucosicola are available with the online version of this paper. aligned using BioEdit version 7.0.5.3 (Hall, 1999) and a 015016 G 2010 IUMS Printed in Great Britain 1527 T. Clavel and others rooted tree was constructed using the neighbour-joining 16S rRNA gene sequence similarity values with members of method with CLUSTAL X version 1.8. Bootstrap values were these genera of ,94 %. calculated on the basis of 1000 resamplings. The max- The gyrase B gene of strain B7T was amplified as described imum-parsimony method was used to confirm the previously (Santos & Ochman, 2004). Amplicons topology of the phylogeny. Fig. 1 gives a current (1500 bp) were purified using agarose gel electrophoresis phylogenetic overview of the family Coriobacteriaceae and and the Wizard SV Gel and PCR Clean-Up System the position of strain B7T. Sequence similarity values were (Promega). Purified products were sequenced using the obtained with the DNA distance matrix function in the primers gyrBBNDN1 (59-CCGTCCACGTCGGCRTCNG- BioEdit software. The 16S rRNA gene sequence of strain YCAT-39) and gyrBBAUP2 (59-GCGGAAGCGGCCNGSN- B7T (1336 bp) was related most closely (.99 %) to ATGTA-39). The gyrase B gene sequence of strain B7T sequences originating from as-yet-uncultured mouse shared 95.7 and 79.3 % similarity with sequences from E. intestinal bacteria (Ley et al., 2005, 2006) and E. mucosicola mucosicola Mt1B8T (GenBank accession no. EU594341) and Mt1B8T (97.6 %). Lower similarities were found to Eggerthella lenta DSM 2243T (EU594342; 524 bp), respec- sequences from Asaccharobacter celatus do03T (93.4 %), tively. Strain B7T exhibited low DNA–DNA relatedness to E. Adlercreutzia equolifaciens FJC-B9T (93.3 %) and two mucosicola DSM 19490T (28.0±2.0 %, two experiments), Eggerthella strains (,90 %). The resolution of 16S rRNA which supported the fact that these two bacteria belong to gene sequence analysis does not allow the identification of different species. The DNA G+C content of strain B7T closely related species. However, it consistently depicts (64.5 mol%) was comparable to those reported in the phylogenetic relationships from the level of domains to literature for its phylogenetic neighbours. moderately related species (Stackebrandt & Goebel, 1994). It has been proposed that a genus could be defined as The results of phenotypic and chemotaxonomic analyses containing species that have 95 % 16S rRNA gene sequence are given in the species description and in Table 1. The similarity to each other (Rossello-Mora & Amann, 2001). fatty acid profile of strain B7T was similar to that of E. We suggest that strain B7T does not belong to either of the mucosicola DSM 19490T. The diamino acid in the genera Adlercreutzia or Asaccharobacter, as the strain has peptidoglycan was identified as meso-diaminopimelic acid, Fig. 1. Phylogenetic position of strain B7T within the family Coriobacteriaceae, based on a neighbour-joining analysis of 16S rRNA gene sequences (1338 bp). Bootstrap values based on 1000 resamplings are shown at branch nodes. Hash signs indicate that the corres- ponding nodes were also recovered in the tree generated using the maximum-parsimony method. Eubacterium limosum ATCC 8486T, a member of the phylum Firmicutes, was used as an outgroup. Bar, 10 substitutions per 100 nucleotide positions. 1528 International Journal of Systematic and Evolutionary Microbiology 60 Enterorhabdus caecimuris sp. nov. Table 1. Characteristics that differentiate strain B7T and Table 1. cont. E. mucosicola DSM 19490T Characteristic 1 2 Strains: 1, B7T;2,E. mucosicola DSM 19490T. Data were taken from this study. DMA, Dimethylacetal; DMMK, dimethylmenaquinone; C18 : 1 c9 15.25 16.68 21 MMK, monomethylmenaquinone; R, resistant (MIC .32 mgml ); C18 : 1 c9 DMA 4.94 4.75 ND, not determined. C18 : 1 c11 DMA 0.59 0.56 C18 : 1 c11/t9/t6 4.16 3.83 C c9,12 1.24 1.30 Characteristic 1 2 18 : 2 Diaminopimelic acid meso LL *Data obtained with Rapid ID32A identification system for anaerobes Major menaquinones (%) (bioMe´rieux). MMK-6 60 100 DValues are expressed as mean±SD of six replicates (three DMMK-6 40 0 independent experiments with duplicates). Whole-cell sugars Glucose + 2 Enzyme activities* which so far has been reported only for the peptidoglycan Aminopeptidase 2 + type A1c and three variations of peptidoglycan type A4c. Glutamic acid + 2 The quinones were monomethylmenaquinone-6 (60 %) decarboxylase and dimethylmenaquinone-6 (40 %). Isoflavone conversion T + For polar lipid analysis, batch cultures (1.5 l) of strain B7 Daidzein 2 T Genistein ND + and E. mucosicola DSM 19490 were grown under anoxic [ Antibiotic MIC (mgml21)D conditions for 48 h in GYBHIc brain–heart infusion broth 21 Cefotaxime R (.32) 1.250±0.112 (no. 211059; BD) supplemented with (l ) 4 g glucose, 4 g ] Ciprofloxacin 0.305±0.035 R (.32) yeast extract and 0.05 % (w/v) cysteine and harvested by Clarithromycin ,0.016 ,0.016 centrifugation [5525 g for 10 min at room temperature in Clindamycin 0.105±0.010 ,0.016 500 ml containers using a 4K15C centrifuge (Sigma)]. Erythromycin ,0.016 0.048±0.007 Pellets were resuspended in filter-sterilized PBS [(l distilled 21 Metronidazole 0.016±0.000 0.034±0.004 water) : 8.60 g NaCl, 0.87 g Na2HPO4, 0.40 g KH2PO4; Oxacillin R (36.000±5.750) 4.667±0.667 pH 7.2] and supernatants were centrifuged again as above. Tetracycline 0.120±0.005 0.115±0.007 Resuspended pellets were pooled in 50 ml Falcon tubes and Tobramycin 4.333±0.558 2.667±0.211 centrifuged as above for 15 min. Supernatants were Vancomycin 1.500±0.129 1.333±0.105 discarded first by inverting the tubes and subsequently Cellular fatty acids pipetting the remaining liquid after the tubes had been left iso-C12 : 0 0.36 0.50 to stand for 30 s. Samples were stored at 280 uC prior to C12 : 0 1.21 0.72 shipping on dry ice. Polar lipid analysis was done by the iso-C13 : 0 2 0.15 Identification Service of the DSMZ and Dr B.
Load more

Recommended publications
  • Daidzein Intake Is Associated with Equol Producing Status Through an Increase in the Intestinal Bacteria Responsible for Equol Production
    Article Daidzein Intake Is Associated with Equol Producing Status through an Increase in the Intestinal Bacteria Responsible for Equol Production Chikara Iino 1, Tadashi Shimoyama 2,*, Kaori Iino 3, Yoshihito Yokoyama 3, Daisuke Chinda 1, Hirotake Sakuraba 1, Shinsaku Fukuda 1 and Shigeyuki Nakaji 4 1 Department of Gastroenterology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan; [email protected] (C.I.); [email protected] (D.C.); [email protected] (H.S.); [email protected] (S.F.) 2 Aomori General Health Examination Center, Aomori 030-0962, Japan 3 Department of Obstetrics and Gynecology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan; [email protected] (K.I.); [email protected] (Y.Y.) 4 Department of Social Medicine, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-017-741-2336 Received: 9 January 2019; Accepted: 7 February 2019; Published: 19 February 2019 Abstracts: Equol is a metabolite of isoflavone daidzein and has an affinity to estrogen receptors. Although equol is produced by intestinal bacteria, the association between the status of equol production and the gut microbiota has not been fully investigated. The aim of this study was to compare the intestinal bacteria responsible for equol production in gut microbiota between equol producer and non-producer subjects regarding the intake of daidzein. A total of 1044 adult subjects who participated in a health survey in Hirosaki city were examined. The concentration of equol in urine was measured by high-performance liquid chromatography.
    [Show full text]
  • WO 2018/064165 A2 (.Pdf)
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
    [Show full text]
  • Isolation of Human Intestinal Bacteria Capable of Producing the Bioactive Metabolite Isourolithin a from Ellagic Acid
    fmicb-08-01521 August 3, 2017 Time: 15:13 # 1 ORIGINAL RESEARCH published: 07 August 2017 doi: 10.3389/fmicb.2017.01521 Isolation of Human Intestinal Bacteria Capable of Producing the Bioactive Metabolite Isourolithin A from Ellagic Acid María V. Selma1*, David Beltrán1, María C. Luna1, María Romo-Vaquero1, Rocío García-Villalba1, Alex Mira2, Juan C. Espín1 and Francisco A. Tomás-Barberán1* 1 Laboratory of Food and Health, Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, Centre for Applied Soil Science and Biology of the Segura – Spanish National Research Council, Murcia, Spain, 2 Department of Health and Genomics, Center for Advanced Research in Public Health, FISABIO Foundation, Valencia, Spain Urolithins are intestinal microbial metabolites produced from ellagitannin- and ellagic Edited by: acid-containing foods such as walnuts, strawberries, and pomegranates. These Rebeca Martín, metabolites, better absorbed than their precursors, can contribute significantly to the INRA Centre Jouy-en-Josas, France beneficial properties attributed to the polyphenols ellagitannins and ellagic acid (EA). Reviewed by: Filomena Nazzaro, However, both the ability of producing the final metabolites in this catabolism (urolithins Consiglio Nazionale delle Ricerche A, B and isourolithin A) and the health benefits associated with ellagitannin consumption (CNR), Italy Francisco José Pérez-Cano, differ considerably among individuals depending on their gut microbiota composition. University of Barcelona, Spain Three human urolithin metabotypes have been previously described, i.e., metabotype *Correspondence: 0 (urolithin non-producers), metabotype A (production of urolithin A as unique final María V. Selma urolithin) and metabotype B (urolithin B and/or isourolithin A are produced besides [email protected] Francisco A.
    [Show full text]
  • Bacterial Involvements in Ulcerative Colitis: Molecular and Microbiological Studies
    BACTERIAL INVOLVEMENTS IN ULCERATIVE COLITIS: MOLECULAR AND MICROBIOLOGICAL STUDIES Samia Alkhalil A thesis submitted in partial fulfilment of the requirements for the award of the degree of Doctor of Philosophy of the University of Portsmouth Institute of Biomedical and biomolecular Sciences School of Pharmacy and Biomedical Sciences October 2017 AUTHORS’ DECLARATION I declare that whilst registered as a candidate for the degree of Doctor of Philosophy at University of Portsmouth, I have not been registered as a candidate for any other research award. The results and conclusions embodied in this thesis are the work of the named candidate and have not been submitted for any other academic award. Samia Alkhalil I ABSTRACT Inflammatory bowel disease (IBD) is a series of disorders characterised by chronic intestinal inflammation, with the principal examples being Crohn’s Disease (CD) and ulcerative colitis (UC). A paradigm of these disorders is that the composition of the colon microbiota changes, with increases in bacterial numbers and a reduction in diversity, particularly within the Firmicutes. Sulfate reducing bacteria (SRB) are believed to be involved in the etiology of these disorders, because they produce hydrogen sulfide which may be a causative agent of epithelial inflammation, although little supportive evidence exists for this possibility. The purpose of this study was (1) to detect and compare the relative levels of gut bacterial populations among patients suffering from ulcerative colitis and healthy individuals using PCR-DGGE, sequence analysis and biochip technology; (2) develop a rapid detection method for SRBs and (3) determine the susceptibility of Desulfovibrio indonesiensis in biofilms to Manuka honey with and without antibiotic treatment.
    [Show full text]
  • Impact of the Interplay Between Bile Acids, Lipids, Intestinal Coriobacteriaceae and Diet on Host Metabolism
    Technische Universität München ZIEL – Zentralinstitut für Ernährungs- und Lebensmittelforschung Nachwuchsgruppe Intestinales Mikrobiom Impact of the interplay between bile acids, lipids, intestinal Coriobacteriaceae and diet on host metabolism Sarah Just Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigten Dissertation. Vorsitzender: Prof. Dr. rer. nat. Siegfried Scherer Prüfer der Dissertation: 1. Prof. Dr. rer. nat. Dirk Haller 2. Prof. Dr. rer. nat. Martin Klingenspor Die Dissertation wurde am 14.02.2017 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 12.06.2017 angenommen. Abstract Abstract The gut microbiome is a highly diverse ecosystem which influences host metabolism via for instance via conversion of bile acids and production of short chain fatty acids. Changes in gut microbiota profiles are associated with metabolic diseases such as obesity, type-2 diabetes, and non-alcoholic fatty liver disease. However, beyond alteration of the ecosystem structure, only a handful of specific bacterial species were shown to influence host metabolism and knowledge about molecular mechanisms by which gut bacteria regulate host metabolism are scant. The family Coriobacteriaceae (phylum Actinobacteria) comprises dominant members of the human gut microbiome and can metabolize cholesterol-derived substrates such as bile acids. Furthermore, their occurrence has been associated with alterations of lipid and cholesterol metabolism. However, consequences for the host are unknown. Hence, the aim of the present study was to characterize the impact of Coriobacteriaceae on lipid, cholesterol, and bile acid metabolism in vivo.
    [Show full text]
  • Quantification of Slackia and Eggerthella Spp. in Human Feces
    fmicb-07-00658 May 5, 2016 Time: 16:44 # 1 View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 09 May 2016 doi: 10.3389/fmicb.2016.00658 Quantification of Slackia and Eggerthella spp. in Human Feces and Adhesion of Representatives Strains to Caco-2 Cells Gyu-Sung Cho1, Felix Ritzmann2, Marie Eckstein2, Melanie Huch2, Karlis Briviba3, Diana Behsnilian4, Horst Neve1 and Charles M. A. P. Franz1* 1 Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany, 2 Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany, 3 Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut, Edited by: Federal Research Institute of Nutrition and Food, Karlsruhe, Germany, 4 Department of Food Technology and Bioprocess Andrea Gomez-Zavaglia, Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany Center for Research and Development in Food Cryotechnology – Consejo Nacional Eggerthella and Slackia spp. are gut associated bacteria that have been suggested to De Investigaciones Científicas Y play roles in host lipid and xenobiotic metabolism. A quantitative PCR method for the Técnicas, Argentina selective enumeration of bacteria belonging to either the genus Eggerthella or Slackia Reviewed by: was developed in order to establish the numbers of these bacteria occurring in human Paula Carasi, Universidad Nacional de La Plata, feces. The primers developed for selective amplification of these genera were tested first Argentina in conventional PCR to test for their specificity.
    [Show full text]
  • Dietary Isoflavones and Intestinal Microbiota: Metabolism and Transformation Into Bioactive Compounds
    In: Isoflavones Biosynthesis, Occurence and Health Effects ISBN: 978-1-61728-113-6 Editor: Melanie J. Thompson, pp. 137-161 © 2010 Nova Science Publishers, Inc. The exclusive license for this PDF is limited to personal printing only. No part of this digital document may be reproduced, stored in a retrieval system or transmitted commercially in any form or by any means. The publisher has taken reasonable care in the preparation of this digital document, but makes no expressed or implied warranty of any kind and assumes no responsibility for any errors or omissions. No liability is assumed for incidental or consequential damages in connection with or arising out of information contained herein. This digital document is sold with the clear understanding that the publisher is not engaged in rendering legal, medical or any other professional services. Chapter IV Dietary Isoflavones and Intestinal Microbiota: Metabolism and Transformation into Bioactive Compounds Maddalena Rossi*, Alberto Amaretti, Lucia Roncaglia, Alan Leonardi and Stefano Raimondi Dept. Chemistry, University of Modena and Reggio Emilia, Italy Abstract Edible plants provide the human with hundreds of non-nutritional phytochemicals which are recognized as beneficial, such as isoflavones. Likewise other polyphenols, isoflavones may undergo extensive transformations during passage through human digestive tract, especially in the colon, where members of the complex commensal microbiota are capable to carry out synergistically a broad range of metabolic transformations affecting the fate and the biological activity of phytochemicals. Diverse bacterial species occurring in the large intestine hydrolyze the glucose conjugated forms of isoflavones, releasing the corresponding aglycones, which may undergo further microbial conversions (especially reductions) giving rise to a wide spectrum of isoflavone-derived compounds.
    [Show full text]
  • Genome-Based Taxonomic Classification of the Phylum
    ORIGINAL RESEARCH published: 22 August 2018 doi: 10.3389/fmicb.2018.02007 Genome-Based Taxonomic Classification of the Phylum Actinobacteria Imen Nouioui 1†, Lorena Carro 1†, Marina García-López 2†, Jan P. Meier-Kolthoff 2, Tanja Woyke 3, Nikos C. Kyrpides 3, Rüdiger Pukall 2, Hans-Peter Klenk 1, Michael Goodfellow 1 and Markus Göker 2* 1 School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom, 2 Department Edited by: of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Martin G. Klotz, Germany, 3 Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States Washington State University Tri-Cities, United States The application of phylogenetic taxonomic procedures led to improvements in the Reviewed by: Nicola Segata, classification of bacteria assigned to the phylum Actinobacteria but even so there remains University of Trento, Italy a need to further clarify relationships within a taxon that encompasses organisms of Antonio Ventosa, agricultural, biotechnological, clinical, and ecological importance. Classification of the Universidad de Sevilla, Spain David Moreira, morphologically diverse bacteria belonging to this large phylum based on a limited Centre National de la Recherche number of features has proved to be difficult, not least when taxonomic decisions Scientifique (CNRS), France rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft *Correspondence: Markus Göker genome sequences
    [Show full text]
  • A Microbiomic Approach to the Characterization of the Impacts and Influences of Viral, Bacterial, and Harmful Algal Bloom Toxins on the Bottlenose Dolphin
    The University of Southern Mississippi The Aquila Digital Community Dissertations Fall 12-2016 A Microbiomic Approach to the Characterization of the Impacts and Influences of Viral, Bacterial, and Harmful Algal Bloom Toxins on the Bottlenose Dolphin Corey David Russo University of Southern Mississippi Follow this and additional works at: https://aquila.usm.edu/dissertations Part of the Animal Sciences Commons, Biology Commons, Diseases Commons, Ecology and Evolutionary Biology Commons, Genetics and Genomics Commons, Immunology and Infectious Disease Commons, Microbiology Commons, and the Pharmacology, Toxicology and Environmental Health Commons Recommended Citation Russo, Corey David, "A Microbiomic Approach to the Characterization of the Impacts and Influences of Viral, Bacterial, and Harmful Algal Bloom Toxins on the Bottlenose Dolphin" (2016). Dissertations. 898. https://aquila.usm.edu/dissertations/898 This Dissertation is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Dissertations by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. A MICROBIOMIC APPROACH TO THE CHARACTERIZATION OF THE IMPACTS AND INFLUENCES OF VIRAL, BACTERIAL, AND HARMFUL ALGAL BLOOM TOXINS ON THE BOTTLENOSE DOLPHIN by Corey David Russo A Dissertation Submitted to the Graduate School and the School of Ocean Science and Technology at The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Approved: ________________________________________________ Dr. Darrell J. Grimes, Committee Chair Professor, Ocean Science and Technology ________________________________________________ Dr. Jeffrey M. Lotz, Committee Member Professor, Ocean Science and Technology ________________________________________________ Dr. Robert J. Griffitt, Committee Member Assistant Professor, Ocean Science and Technology ________________________________________________ Dr.
    [Show full text]
  • Biomolecules
    biomolecules Article Metabolism of Soy Isoflavones by Intestinal Bacteria: Genome Analysis of an Adlercreutzia equolifaciens Strain That Does Not Produce Equol Lucía Vázquez 1,2, Ana Belén Flórez 1,2 , Begoña Redruello 3 and Baltasar Mayo 1,2,* 1 Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), 33300 Villaviciosa, Spain; [email protected] (L.V.); abfl[email protected] (A.B.F.) 2 Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain 3 Servicios Científico-Técnicos, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), 33300 Villaviciosa, Spain; [email protected] * Correspondence: [email protected]; Tel.: +34-985-89-33-45 Received: 17 April 2020; Accepted: 20 June 2020; Published: 23 June 2020 Abstract: Isoflavones are transformed in the gut into more estrogen-like compounds or into inactive molecules. However, neither the intestinal microbes nor the pathways leading to the synthesis of isoflavone-derived metabolites are fully known. In the present work, 73 fecal isolates from three women with an equol-producing phenotype were considered to harbor equol-related genes by qPCR. After typing, 57 different strains of different taxa were tested for their ability to act on the isoflavones daidzein and genistein. Strains producing small to moderate amounts of dihydrodaidzein and/or O-desmethylangolensin (O-DMA) from daidzein and dihydrogenistein from genistein were recorded. However, either alone or in several strain combinations, equol producers were not found, even though one of the strains, W18.34a (also known as IPLA37004), was identified as Adlercreutzia equolifaciens, a well-described equol-producing species.
    [Show full text]
  • Intestinal Microbiota As a Tetrahydrobiopterin Exogenous
    www.nature.com/scientificreports OPEN Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice Received: 22 June 2016 Jaques Belik1,2, Yulia Shifrin1, Erland Arning3, Teodoro Bottiglieri3, Jingyi Pan1, Accepted: 29 November 2016 Michelle C. Daigneault4 & Emma Allen-Vercoe4 Published: 12 January 2017 Tetrahydrobiopterin (BH4) is a cofactor of a number of regulatory enzymes. Although there are no known BH4 exogenous sources, the tissue content of this biopterin increases with age in GTP cyclohydrolase 1-deficient hyperphenylalaninemia-1 (hph-1) mice. Since certain bacteria are known to generate BH4, we hypothesize that generation of this biopterin by the intestinal microbiota contributes to its tissue increase in hph-1 adult mice. The goal of this study was to comparatively evaluate hph-1 mice and wild-type C57Bl/6 controls for the presence of intestinal BH4-producing bacteria. Newborn and adult mice fecal material was screened for 6-pyruvoyltetrahydropterin synthase (PTPS-2) an enzyme only present in BH4-generating bacteria. Adult, but not newborn, wild-type control and hph-1 mouse fecal material contained PTPS-2 mRNA indicative of the presence of BH4-generating bacteria. Utilizing chemostat-cultured human fecal bacteria, we identified the PTPS-2-producing bacteria as belonging to the Actinobacteria phylum. We further confirmed that at least two PTPS-2-producing species, Adlercreutzia equolifaciens and Microbacterium schleiferi, generate BH4 and are present in hph-1 fecal material. In conclusion, intestinal Actinobacteria generate BH4. This finding has important translational significance, since manipulation of the intestinal flora in individuals with congenital biopterin deficiency may allow for an increase in total body BH4 content.
    [Show full text]
  • High-Throughput Sequencing of the Chicken Gut Microbiome
    High-throughput sequencing of the chicken gut microbiome By Nicholas Andrew Duggett A thesis submitted to The University of Birmingham For the degree of DOCTOR OF PHILOSOPHY School of Biosciences The University of Birmingham August 2015 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. Abstract The chicken (Gallus gallus domesticus) is the most abundant and widely distributed livestock animal with a global population of over 21 billion. A commercially raised broiler chick takes five-weeks to reach market weight and this can be attributed to the selection of genetic traits, better feed formulation (in addition to enzyme supplementation) and an increased understanding of health and husbandry. The symbiotic, complex and variable community of the microbiome forms an important part of the gastrointestinal tract (gut) and is involved in gut-development and non-specific resistance to infection. This study investigated the chicken gut microbiota using high-throughput 16S rRNA sequencing on an Illumina MiSeq and culture-based techniques. There was specific interest in the proventriculus of which there is limited research currently in the literature and the caecum because it contains the highest density of bacterial cells in the gut at 1011 cells per gram.
    [Show full text]